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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $species_info = array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ) $local_species = 'shi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $species_info = array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ) $local_species = 'shi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ), 'gf_id' => 'HOM05D001249', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001249' ), 'data_identifier' => 'HOM05D001249', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001249', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p24660' => 'bna', 'A03p25490' => 'bna', 'A04p33180' => 'bna', 'A04p34290' => 'bna', 'A05p01670' => 'bna', 'A08p37750' => 'bna', 'Aa31LG1G10800' => 'aar', 'Aa31LG1G25730' => 'aar', 'Aa31LG1G27540' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2490' => 'aag', 'Actinidia02817' => 'ach', 'Actinidia20166' => 'ach', 'Ah.05g180130' => 'amhyb', 'Ah.07g203310' => 'amhyb', 'AL1G10940' => 'aly', 'AL4G42930' => 'aly', 'AL4G45390' => 'aly', 'Aqoxy1G00144' => 'aox', 'Aqoxy2G03633' => 'aox', 'Aqoxy5G02073' => 'aox', 'Aqoxy5G03616' => 'aox', 'Aqoxy6G00001' => 'aox', 'Aqoxy6G00880' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4U54KW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K3X9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AI0VCX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GD18YF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GR5MMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L9LT8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P4KHGY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R434E2' => 'arhy', 'AT1G01470' => 'ath', 'AT2G44060' => 'ath', 'AT2G46140' => 'ath', 'ATR0099G032' => 'atr', 'ATR0225G022' => 'atr', 'ATR0721G031' => 'atr', 'ATR0743G044' => 'atr', 'ATR0762G011' => 'atr', 'Atru.chr2.3352' => 'acertr', 'Atru.chr3.1961' => 'acertr', 'Atru.chr5.566' => 'acertr', 'Atru.chr5.585' => 'acertr', 'AUR62002497' => 'cqu', 'AUR62004416' => 'cqu', 'AUR62022622' => 'cqu', 'AUR62022623' => 'cqu', 'AUR62023689' => 'cqu', 'BcaB01g03236' => 'bca', 'BcaB01g03333' => 'bca', 'BcaB01g03343' => 'bca', 'BcaB01g06149' => 'bca', 'BcaB03g13520' => 'bca', 'BcaB06g29354' => 'bca', 'BcaB06g29513' => 'bca', 'BcaC01g05092' => 'bca', 'BcaC01g05189' => 'bca', 'BcaC02g07023' => 'bca', 'BcaC02g07138' => 'bca', 'BcaC02g12496' => 'bca', 'BcaC02g12711' => 'bca', 'BcaC07g42784' => 'bca', 'BolC3t12567H' => 'bol', 'BolC3t15287H' => 'bol', 'BolC3t15390H' => 'bol', 'BolC4t28588H' => 'bol', 'BraA03t11672Z' => 'bra', 'BraA03t11767Z' => 'bra', 'BraA04t18777Z' => 'bra', 'BraA04t18890Z' => 'bra', 'BraA05t19163Z' => 'bra', 'BraA08t35672Z' => 'bra', 'C03p00060' => 'bna', 'C03p29400' => 'bna', 'C03p30420' => 'bna', 'C04p01910' => 'bna', 'C04p70870' => 'bna', 'C04p72110' => 'bna', 'CAN.G17668.1' => 'can', 'CAN.G207.8' => 'can', 'CAN.G3870.1' => 'can', 'CAN.G68.1' => 'can', 'CAN.G78.132' => 'can', 'CAN.G91.11' => 'can', 'CANSAT56G1473' => 'cansat', 'CANSAT56G2692' => 'cansat', 'CARHR000900' => 'chi', 'CARHR139220' => 'chi', 'CARHR141420' => 'chi', 'Carub.0001s0077' => 'cru', 'Carub.0004s2661' => 'cru', 'Carub.0004s2882' => 'cru', 'Ca_06180_v3' => 'car', 'Ca_07945_v3' => 'car', 'Ca_26658_v3' => 'car', 'CBR_g39190' => 'cbr', 'CBR_g55417' => 'cbr', 'CBR_g75560' => 'cbr', 'Cc02_g38620' => 'ccan', 'Cc03_g16190' => 'ccan', 'CDE02G4753' => 'cde', 'CDE04G1250' => 'cde', 'CDE04G1507' => 'cde', 'CDE07G0014' => 'cde', 'CDE09G1295' => 'cde', 'Cfa003866' => 'cfa', 'Cfa003867' => 'cfa', 'Cfa005667' => 'cfa', 'Cfa007551' => 'cfa', 'Cfa007552' => 'cfa', 'Cfa008531' => 'cfa', 'Cfa012405' => 'cfa', 'Ciclev10010508m.g' => 'ccl', 'Ciclev10020871m.g' => 'ccl', 'Ciclev10023843m.g' => 'ccl', 'CiPaw.01G068200' => 'cil', 'CiPaw.01G202900' => 'cil', 'CiPaw.02G035700' => 'cil', 'CiPaw.02G125500' => 'cil', 'ClCG05G001200' => 'cla', 'ClCG06G010080' => 'cla', 'COL.COLO4_12782' => 'col', 'COL.COLO4_32523' => 'col', 'Cpa.g.sc11.66' => 'cpa', 'Cpa.g.sc11.68' => 'cpa', 'Cpa.g.sc11.69' => 'cpa', 'Cpa.g.sc9.242' => 'cpa', 'CsaV3_2G011930' => 'csa', 'CsaV3_3G008590' => 'csa', 'CSS0027600' => 'camsi', 'CSS0028444' => 'camsi', 'CSS0034761' => 'camsi', 'DCAR_005362' => 'dca', 'DCAR_006950' => 'dca', 'DCAR_023793' => 'dca', 'DCAR_025218' => 'dca', 'DCAR_025219' => 'dca', 'DCAR_025220' => 'dca', 'DCAR_027489' => 'dca', 'Dinv24741' => 'din', 'Dinv32524' => 'din', 'Dinv43867' => 'din', 'Duzib093G0930' => 'dzi', 'Duzib138G0540' => 'dzi', 'ECA233G0816' => 'eca', 'ECA233G4379' => 'eca', 'ECA236G1734' => 'eca', 'ECA236G2695' => 'eca', 'ECA236G5025' => 'eca', 'ECA238G0673' => 'eca', 'ECA248G2519' => 'eca', 'EL10Ac1g00350' => 'bvu', 'EL10Ac1g00351' => 'bvu', 'EL10Ac3g06181' => 'bvu', 'Eucgr.D02327' => 'egr', 'Eucgr.H00245' => 'egr', 'FAN01G2548' => 'fan', 'FAN03G0166' => 'fan', 'FAN03G1093' => 'fan', 'FAN06G0946' => 'fan', 'FAN06G1373' => 'fan', 'FAN06G1939' => 'fan', 'FAN06G3516' => 'fan', 'FAN06G3801' => 'fan', 'FAN06G4194' => 'fan', 'FAN06G4990' => 'fan', 'FAN10G0303' => 'fan', 'FAN10G1427' => 'fan', 'FAN10G3091' => 'fan', 'FAN10G3267' => 'fan', 'FAN26G0381' => 'fan', 'FAN28G2707' => 'fan', 'FvH4_1g00090' => 'fve', 'FvH4_4g03320' => 'fve', 'FvH4_7g15440' => 'fve', 'FvH4_7g15460' => 'fve', 'FvH4_7g15470' => 'fve', 'FvH4_7g31461' => 'fve', 'Glyma.02G277300' => 'gma', 'Glyma.09G254302' => 'gma', 'Glyma.14G037300' => 'gma', 'Glyma.16G031300' => 'gma', 'Glyma.18G238700' => 'gma', 'Glyma.20G044800' => 'gma', 'Gohir.A01G231800' => 'ghi', 'Gohir.A03G218500' => 'ghi', 'Gohir.A07G140200' => 'ghi', 'Gohir.A07G233300' => 'ghi', 'Gohir.A08G127951' => 'ghi', 'Gohir.A08G253400' => 'ghi', 'Gohir.A11G092600' => 'ghi', 'Gohir.D01G221900' => 'ghi', 'Gohir.D07G145400' => 'ghi', 'Gohir.D11G097400' => 'ghi', 'Gorai.001G157400' => 'gra', 'Gorai.002G268600' => 'gra', 'Gorai.007G103700' => 'gra', 'GSVIVG01026974001' => 'vvi', 'GSVIVG01026975001' => 'vvi', 'GSVIVG01026976001' => 'vvi', 'GSVIVG01038264001' => 'vvi', 'HanXRQChr01g0017591' => 'han', 'HanXRQChr04g0120831' => 'han', 'HanXRQChr16g0523701' => 'han', 'HanXRQChr17g0562311' => 'han', 'Haze_15569' => 'cav', 'Hma1.2p1_0335F.1_g128850' => 'hma', 'Hma1.2p1_0623F.1_g191120' => 'hma', 'HPP92_001207' => 'vpl', 'HPP92_005479' => 'vpl', 'Hund12304' => 'sun', 'Hund27240' => 'sun', 'Lalb_Chr04g0249331' => 'lal', 'Lalb_Chr08g0233291' => 'lal', 'Lalb_Chr10g0096611' => 'lal', 'Lalb_Chr10g0106081' => 'lal', 'Lalb_Chr11g0073301' => 'lal', 'Lalb_Chr15g0080151' => 'lal', 'Lalb_Chr23g0275981' => 'lal', 'Lj1g0025696' => 'lja', 'Lj3g0021395' => 'lja', 'Lj6g0018713' => 'lja', 'Lj7A506T71' => 'lonja', 'Lj9C589T9' => 'lonja', 'Lj9C590T13' => 'lonja', 'LjContig00564g0000582' => 'lja', 'Lju124C5T8' => 'lonja', 'Lju41A14T32' => 'lonja', 'Lju470C1T4' => 'lonja', 'Lsat_1_v5_gn_1_82580' => 'lsa', 'Lsat_1_v5_gn_4_35200' => 'lsa', 'Lsat_1_v5_gn_7_2601' => 'lsa', 'Lsat_1_v5_gn_7_2621' => 'lsa', 'Lsat_1_v5_gn_7_2641' => 'lsa', 'Manes.01G009601' => 'mes', 'Manes.01G252100' => 'mes', 'Manes.05G028700' => 'mes', 'Manes.05G208200' => 'mes', 'Mapoly0002s0220' => 'mpo', 'Mapoly0065s0058' => 'mpo', 'MBI06_g33540_MAGBIO' => 'mbi', 'MBI07_g27882_MAGBIO' => 'mbi', 'MBI10_g03654_MAGBIO' => 'mbi', 'MBI16_g27589_MAGBIO' => 'mbi', 'MD01G1071800' => 'mdo', 'MD01G1071900' => 'mdo', 'MD01G1072000' => 'mdo', 'MD02G1000600' => 'mdo', 'MD07G1130800' => 'mdo', 'MD07G1130900' => 'mdo', 'MD15G1142200' => 'mdo', 'Medtr3g045190' => 'mtr', 'Medtr5g088850' => 'mtr', 'Medtr7g079180' => 'mtr', 'Medtr8g028480' => 'mtr', 'MELO3C006079.2' => 'cme', 'MELO3C020416.2' => 'cme', 'Migut.B01802' => 'egut', 'Migut.G00799' => 'egut', 'Migut.H01873' => 'egut', 'Migut.M01824' => 'egut', 'Migut.N03015' => 'egut', 'MSTRG.12260' => 'ama', 'MSTRG.14404' => 'ama', 'MSTRG.20864' => 'ama', 'MSTRG.8086' => 'ama', 'Nitab4.5_0000348g0040' => 'nta', 'Nitab4.5_0000915g0090' => 'nta', 'Nitab4.5_0000915g0100' => 'nta', 'Nitab4.5_0003501g0080' => 'nta', 'Nitab4.5_0003681g0020' => 'nta', 'Nitab4.5_0004481g0030' => 'nta', 'Nitab4.5_0005148g0040' => 'nta', 'Nitab4.5_0006083g0030' => 'nta', 'Nitab4.5_0010695g0040' => 'nta', 'Nn1g01694' => 'nnu', 'Nn1g09415' => 'nnu', 'Nn5g29337' => 'nnu', 'Nn6g33248' => 'nnu', 'Oeu004908.1' => 'oeu', 'Oeu014978.1' => 'oeu', 'Oeu054357.1' => 'oeu', 'Oeu054358.1' => 'oeu', 'Os01g0225600' => 'osa', 'Os01g0624400' => 'osa', 'Os03g0843300' => 'osa', 'Os05g0584200' => 'osa', 'Os07g0272300' => 'osa', 'Peaxi162Scf00020g00154' => 'pax', 'Peaxi162Scf00057g01912' => 'pax', 'Peaxi162Scf00057g01913' => 'pax', 'Peaxi162Scf00585g00514' => 'pax', 'Peaxi162Scf01205g00175' => 'pax', 'Peaxi162Scf63976g00001' => 'pax', 'PGR031G3681' => 'pgr', 'PGR142G4250' => 'pgr', 'PGSC0003DMG400000066' => 'stu', 'PGSC0003DMG400000067' => 'stu', 'PGSC0003DMG400006460' => 'stu', 'PGSC0003DMG400013715' => 'stu', 'PGSC0003DMG400019407' => 'stu', 'Phvul.006G018100' => 'pvu', 'Phvul.008G057900' => 'pvu', 'Phvul.008G203600' => 'pvu', 'Phvul.010G104800' => 'pvu', 'Potri.002G165000' => 'ptr', 'Potri.007G146300' => 'ptr', 'Potri.014G090800' => 'ptr', 'Pp3c22_13190' => 'ppa', 'Pp3c23_18440' => 'ppa', 'Pp3c24_14840' => 'ppa', 'Prupe.2G178000' => 'ppe', 'Prupe.2G178100' => 'ppe', 'Prupe.2G178200' => 'ppe', 'Prupe.2G178300' => 'ppe', 'Prupe.7G271000' => 'ppe', 'Psat2g021400' => 'psa', 'Psat3g105280' => 'psa', 'Psat4g157760' => 'psa', 'Psat4g157880' => 'psa', 'PSO135G0119' => 'pso', 'PSO151G0033' => 'pso', 'PSO170G3486' => 'pso', 'PSO266G0008' => 'pso', 'PSO304G0001' => 'pso', 'PSO304G0013' => 'pso', 'PSO304G0017' => 'pso', 'PSO304G0018' => 'pso', 'PSO304G0019' => 'pso', 'PSO384G0080' => 'pso', 'PSO384G1150' => 'pso', 'PSO384G1265' => 'pso', 'PSO384G2830' => 'pso', 'PSO384G3115' => 'pso', 'PSO384G3429' => 'pso', 'PSO384G4681' => 'pso', 'PSO541G5475' => 'pso', 'PSO675G8641' => 'pso', 'PSO724G1354' => 'pso', 'QL04p055662' => 'qlo', 'QL04p055693' => 'qlo', 'QL10p064706' => 'qlo', 'QL10p064865' => 'qlo', 'QL10p064899' => 'qlo', 'QL10p065831' => 'qlo', 'RcHm_v2.0_Chr1g0357761' => 'rch', 'RcHm_v2.0_Chr1g0357771' => 'rch', 'RcHm_v2.0_Chr1g0357781' => 'rch', 'RcHm_v2.0_Chr2g0084381' => 'rch', 'Rhsim01G0166300' => 'rsi', 'Rhsim01G0166700' => 'rsi', 'Rhsim05G0174500' => 'rsi', 'Rhsim07G0009700' => 'rsi', 'Sabra02G0146500' => 'sbr', 'Sabra07G0115100' => 'sbr', 'Sabra14G0065800' => 'sbr', 'SalBow3G0488' => 'sbo', 'SalBow6G0898' => 'sbo', 'SalBow7G0650' => 'sbo', 'Sc01g0003190' => 'sci', 'Sc25g0002220' => 'sci', 'Sed0002172' => 'sed', 'Sed0007404' => 'sed', 'Sed0017883' => 'sed', 'Sed0022992' => 'sed', 'SEGI_02724' => 'sgi', 'SEGI_07775' => 'sgi', 'SEGI_14385' => 'sgi', 'SEGI_24564' => 'sgi', 'SGA_v2.0_scaffold12G06226' => 'sas', 'SGA_v2.0_scaffold150G36630' => 'sas', 'SGA_v2.0_scaffold266G46145' => 'sas', 'SGA_v2.0_scaffold37G14908' => 'sas', 'SGA_v2.0_scaffold9G05008' => 'sas', 'SHI01299' => 'shi', 'SHI01452' => 'shi', 'SHI03553' => 'shi', 'SHI13210' => 'shi', 'SHI15069' => 'shi', 'SHI15713' => 'shi', 'SHI22067' => 'shi', 'SHI22212' => 'shi', 'SHI22213' => 'shi', 'SHI23769' => 'shi', 'SHI24409' => 'shi', 'SHI28419' => 'shi', 'SHI28938' => 'shi', 'SHI31027' => 'shi', 'SHI32247' => 'shi', 'SHI32248' => 'shi', 'SHI32657' => 'shi', 'SHI33111' => 'shi', 'SHI33123' => 'shi', 'SHI33268' => 'shi', 'SHI33323' => 'shi', 'SHI33433' => 'shi', 'SHI33715' => 'shi', 'SHI33844' => 'shi', 'SHI34456' => 'shi', 'SHI36402' => 'shi', 'SHI36580' => 'shi', 'SHI37204' => 'shi', 'SHI38076' => 'shi', 'SHI38679' => 'shi', 'SHI40070' => 'shi', 'SHI40100' => 'shi', 'SHI41582' => 'shi', 'SHI42006' => 'shi', 'SHI43834' => 'shi', 'SHI44366' => 'shi', 'SHI45532' => 'shi', 'SHI45970' => 'shi', 'SHI47228' => 'shi', 'SHI48973' => 'shi', 'SHI49507' => 'shi', 'SHI49554' => 'shi', 'SHI49584' => 'shi', 'SHI50079' => 'shi', 'SHI50087' => 'shi', 'SHI50200' => 'shi', 'SHI50201' => 'shi', 'SHI50436' => 'shi', 'SHI51223' => 'shi', 'SHI51414' => 'shi', 'SHI51574' => 'shi', 'SHI51633' => 'shi', 'SHI51778' => 'shi', 'SHI51788' => 'shi', 'SHI51912' => 'shi', 'SHI52789' => 'shi', 'SHI53105' => 'shi', 'SHI53195' => 'shi', 'SHI53212' => 'shi', 'SHI53497' => 'shi', 'SHI53941' => 'shi', 'SHI54170' => 'shi', 'SHI54243' => 'shi', 'SHI54444' => 'shi', 'SHI55027' => 'shi', 'SMO147G0113' => 'smo', 'SMO174G0085' => 'smo', 'SMO334G0106' => 'smo', 'SMO367G0480' => 'smo', 'Solyc01g095140.4' => 'sly', 'Solyc01g095150.3' => 'sly', 'Solyc08g015690.4' => 'sly', 'Solyc10g011900.3' => 'sly', 'Solyc12g017520.1' => 'sly', 'Sopen01g038930' => 'spe', 'Sopen01g038940' => 'spe', 'Sopen08g005800' => 'spe', 'Sopen10g005690' => 'spe', 'Sopen12g008300' => 'spe', 'Sp1g00840' => 'spa', 'Sp4g26140' => 'spa', 'Sp4g28200' => 'spa', 'TAR362G1111' => 'tar', 'TAR374G0414' => 'tar', 'TAR374G1706' => 'tar', 'TAR376G0188' => 'tar', 'TAR629G1937' => 'tar', 'THA.LOC104801390' => 'tha', 'THA.LOC104802350' => 'tha', 'THA.LOC104804361' => 'tha', 'THA.LOC104816436' => 'tha', 'THA.LOC104817042' => 'tha', 'THA.LOC104817321' => 'tha', 'THA.LOC104827606' => 'tha', 'Thecc.01G352000' => 'tca', 'Thecc.05G000700' => 'tca', 'Thhalv10001537m.g' => 'esa', 'Thhalv10001664m.g' => 'esa', 'Thhalv10009011m.g' => 'esa', 'TPR.G11914' => 'tpr', 'TPR.G16415' => 'tpr', 'TPR.G17658' => 'tpr', 'TPR.G28290' => 'tpr', 'TPR.G29570' => 'tpr', 'TWI14G0583' => 'twi', 'TWI63G1312' => 'twi', 'unitig_26.g9972' => 'ugi', 'unitig_899.g15530' => 'ugi', 'vmacro00731' => 'vma', 'vmacro03772' => 'vma', 'vmacro13223' => 'vma', 'vmacro20891' => 'vma', 'vmacro20895' => 'vma', 'vmacro20896' => 'vma', 'VMungo0331G0253' => 'vmu', 'VMungo0540G2213' => 'vmu', 'VMungo0647G1653' => 'vmu', 'VMungo1383G2977' => 'vmu', 'Zm00001eb064120' => 'zma', 'Zm00001eb159430' => 'zma', 'Zm00001eb304760' => 'zma', 'Zm00001eb342130' => 'zma', 'Zm00001eb344820' => 'zma', 'Zm00001eb358640' => 'zma' ) $gf_id = 'HOM05D001249' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001249' ) $data_identifier = 'HOM05D001249' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 6, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 5, 'bca' => (int) 14, 'bol' => (int) 4, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 2, 'cde' => (int) 5, 'cfa' => (int) 7, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 2, 'col' => (int) 2, 'cpa' => (int) 4, 'csa' => (int) 2, 'camsi' => (int) 3, 'dca' => (int) 7, 'din' => (int) 3, 'dzi' => (int) 2, 'eca' => (int) 7, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 6, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 3, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 1, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 7, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 3, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 19, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 5, 'shi' => (int) 65, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 2, 'ugi' => (int) 2, 'vma' => (int) 6, 'vmu' => (int) 4, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb358640' $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